CHANGES.TXT
README.TXT
USAGE.TXT
ez_setup.py
ez_setup.pyc
setup.py
doc/Design.rst
doc/FAQ.rst
doc/Glossary.rst
doc/Introduction.rst
doc/Makefile
doc/Todo.rst
doc/Tutorial.rst
doc/cheatsheet.rst
doc/complicated_example.rst
doc/complicated_example_code.rst
doc/conf.py
doc/contents.rst
doc/history.rst
doc/intermediate_example.rst
doc/intermediate_example_code.rst
doc/make.bat
doc/propset
doc/proxy_logger.rst
doc/sharing_data_across_jobs_example.rst
doc/sharing_data_across_jobs_example_code.rst
doc/simple_tutorial.rst
doc/simpler.rst
doc/task.rst
doc/_templates/index.html
doc/_templates/layout.html
doc/complex_dags/dot/all.dot
doc/complex_dags/dot/non_dag.dot
doc/complex_dags/dot/task17.dot
doc/complex_dags/dot/task17_from_task9.dot
doc/complex_dags/dot/task25_from_task9.dot
doc/complex_dags/jpg/all.jpg
doc/complex_dags/jpg/all_sm.jpg
doc/complex_dags/jpg/non_dag.jpg
doc/complex_dags/jpg/non_dag_sm.jpg
doc/complex_dags/jpg/task17.jpg
doc/complex_dags/jpg/task17_from_task9.jpg
doc/complex_dags/jpg/task17_from_task9_sm.jpg
doc/complex_dags/jpg/task17_sm.jpg
doc/complex_dags/jpg/task25_from_task9.jpg
doc/complex_dags/jpg/task25_from_task9_sm.jpg
doc/complex_dags/png/all.png
doc/complex_dags/png/non_dag.png
doc/complex_dags/png/task17.png
doc/complex_dags/png/task17_from_task9.png
doc/complex_dags/png/task25_from_task9.png
doc/complex_dags/svg/all.svg
doc/complex_dags/svg/non_dag.svg
doc/complex_dags/svg/task17.svg
doc/complex_dags/svg/task17_from_task9.svg
doc/complex_dags/svg/task25_from_task9.svg
doc/example_scripts/complicated_example.py
doc/example_scripts/intermediate_example.py
doc/example_scripts/simpler.py
doc/example_scripts/simpler_with_shared_logging.py
doc/html/.buildinfo
doc/html/Design.html
doc/html/FAQ.html
doc/html/Glossary.html
doc/html/Introduction.html
doc/html/Overview.html
doc/html/Todo.html
doc/html/Tutorial.html
doc/html/cheatsheet.html
doc/html/complicated_example.html
doc/html/complicated_example_code.html
doc/html/contents.html
doc/html/genindex.html
doc/html/history.html
doc/html/index.html
doc/html/intermediate_example.html
doc/html/intermediate_example_code.html
doc/html/modindex.html
doc/html/objects.inv
doc/html/proxy_logger.html
doc/html/search.html
doc/html/searchindex.js
doc/html/sharing_data_across_jobs_example.html
doc/html/sharing_data_across_jobs_example_code.html
doc/html/simple_tutorial.html
doc/html/simpler.html
doc/html/task.html
doc/html/_images/complete.jpg
doc/html/_images/complex_conceptual.jpg
doc/html/_images/complex_file_dag.jpg
doc/html/_images/complex_pypaline.jpg
doc/html/_images/complex_ruffus.jpg
doc/html/_images/cyl_ruffus.jpg
doc/html/_images/force_from_task1.jpg
doc/html/_images/four_stage_pipeline.jpg
doc/html/_images/key.jpg
doc/html/_images/maximal_mode.jpg
doc/html/_images/minimal_mode.jpg
doc/html/_sources/Design.txt
doc/html/_sources/FAQ.txt
doc/html/_sources/Glossary.txt
doc/html/_sources/Introduction.txt
doc/html/_sources/Overview.txt
doc/html/_sources/Todo.txt
doc/html/_sources/Tutorial.txt
doc/html/_sources/cheatsheet.txt
doc/html/_sources/complicated_example.txt
doc/html/_sources/complicated_example_code.txt
doc/html/_sources/contents.txt
doc/html/_sources/history.txt
doc/html/_sources/index.txt
doc/html/_sources/intermediate_example.txt
doc/html/_sources/intermediate_example_code.txt
doc/html/_sources/proxy_logger.txt
doc/html/_sources/sharing_data_across_jobs_example.txt
doc/html/_sources/sharing_data_across_jobs_example_code.txt
doc/html/_sources/simple_tutorial.txt
doc/html/_sources/simpler.txt
doc/html/_sources/task.txt
doc/html/_static/basic.css
doc/html/_static/contents.png
doc/html/_static/default.css
doc/html/_static/doctools.js
doc/html/_static/file.png
doc/html/_static/jquery.js
doc/html/_static/logo.jpg
doc/html/_static/minus.png
doc/html/_static/navigation.png
doc/html/_static/plus.png
doc/html/_static/pygments.css
doc/html/_static/pypaline.css
doc/html/_static/ruffus.css
doc/html/_static/searchtools.js
doc/html/_static/sphinxdoc.css
doc/html/_static/example_scripts/complicated_example.py
doc/html/_static/example_scripts/intermediate_example.py
doc/html/_static/example_scripts/simpler.py
doc/html/_static/example_scripts/simpler_with_shared_logging.py
doc/images/complete.jpg
doc/images/complete.svg
doc/images/complex_conceptual.jpg
doc/images/complex_file_dag.jpg
doc/images/complex_ruffus.jpg
doc/images/cyl_ruffus.jpg
doc/images/force_from_task1.jpg
doc/images/four_stage_pipeline.jpg
doc/images/key.jpg
doc/images/logo.jpg
doc/images/maximal_mode.jpg
doc/images/minimal_mode.jpg
doc/images/src/Backup_of_complex_file_dag.cdr
doc/images/src/Backup_of_complex_pipeline.cdr
doc/images/src/complex_conceptual.cdr
doc/images/src/complex_file_dag.cdr
doc/images/src/complex_pipeline.cdr
doc/images/src/key.cdr
doc/static_data/ruffus.css
doc/static_data/example_scripts/complicated_example.py
doc/static_data/example_scripts/intermediate_example.py
doc/static_data/example_scripts/simpler.py
parameters/IGNORED_FILES
ruffus.egg-info/PKG-INFO
ruffus.egg-info/SOURCES.txt
ruffus.egg-info/dependency_links.txt
ruffus.egg-info/top_level.txt
src/ruffus/__init__.py
src/ruffus/adjacent_pairs_iterate.py
src/ruffus/file_name_parameters.py
src/ruffus/graph.py
src/ruffus/print_dependencies.py
src/ruffus/proxy_logger.py
src/ruffus/ruffus_exceptions.py
src/ruffus/ruffus_utility.py
src/ruffus/ruffus_version.py
src/ruffus/svn-commit.tmp
src/ruffus/task.py
src/ruffus/test/complicated_example.py
src/ruffus/test/create_test_script_from_dependency_tree.py
src/ruffus/test/draw_specified_dependency_tree.py
src/ruffus/test/intermediate_example.py
src/ruffus/test/qrsh_workaround.py
src/ruffus/test/simpler.py
src/ruffus/test/simpler_with_shared_logging.py
src/ruffus/test/test_branching_dependencies.py
src/ruffus/test/test_exceptions.py
src/ruffus/test/test_follows_mkdir.py
src/ruffus/test/test_script.py_template
src/ruffus/test/test_task_file_dependencies.py
src/ruffus/test/test_task_misc.py
src/ruffus/test/test_task_param_factory.py
src/ruffus/test/auto_generated_pipeline_examples/parallel.py
src/ruffus/test/auto_generated_pipeline_examples/simple.py
src/ruffus/test/auto_generated_pipeline_examples/simpler.py
src/ruffus/test/data_for_complicated_example/all_genes_in_each_species/fly.genes.fa
src/ruffus/test/data_for_complicated_example/all_genes_in_each_species/octopus.genes.fa
src/ruffus/test/data_for_complicated_example/all_genes_in_each_species/spider.genes.fa
src/ruffus/test/data_for_complicated_example/all_genes_in_each_species/worm.genes.fa
src/ruffus/test/data_for_complicated_example/unknown_genes/gene_sets1.genes.fa
src/ruffus/test/data_for_complicated_example/unknown_genes/gene_sets2.genes.fa
src/ruffus/test/data_for_intermediate_example/genes/001.gene
src/ruffus/test/data_for_intermediate_example/genes/001.gwas
src/ruffus/test/data_for_intermediate_example/genes/002.gene
src/ruffus/test/data_for_intermediate_example/genes/002.gwas
src/ruffus/test/data_for_intermediate_example/genes/003.gene
src/ruffus/test/data_for_intermediate_example/genes/003.gwas
src/ruffus/test/data_for_intermediate_example/genes/004.gene
src/ruffus/test/data_for_intermediate_example/genes/004.gwas
src/ruffus/test/data_for_intermediate_example/genes/005.gene
src/ruffus/test/data_for_intermediate_example/genes/005.gwas
src/ruffus/test/data_for_intermediate_example/genes/006.gene
src/ruffus/test/data_for_intermediate_example/genes/006.gwas
src/ruffus/test/data_for_intermediate_example/genes/007.gene
src/ruffus/test/data_for_intermediate_example/genes/007.gwas
src/ruffus/test/data_for_intermediate_example/genes/008.gene
src/ruffus/test/data_for_intermediate_example/genes/008.gwas
src/ruffus/test/data_for_intermediate_example/genes/009.gene
src/ruffus/test/data_for_intermediate_example/genes/009.gwas
src/ruffus/test/data_for_intermediate_example/genes/010.gene
src/ruffus/test/data_for_intermediate_example/genes/010.gwas
src/ruffus/test/data_for_intermediate_example/genes/011.gene
src/ruffus/test/data_for_intermediate_example/genes/011.gwas
src/ruffus/test/data_for_intermediate_example/genes/012.gene
src/ruffus/test/data_for_intermediate_example/genes/012.gwas
src/ruffus/test/data_for_intermediate_example/genes/013.gene
src/ruffus/test/data_for_intermediate_example/genes/013.gwas
src/ruffus/test/data_for_intermediate_example/genes/014.gene
src/ruffus/test/data_for_intermediate_example/genes/014.gwas
src/ruffus/test/data_for_intermediate_example/genes/015.gene
src/ruffus/test/data_for_intermediate_example/genes/015.gwas
src/ruffus/test/data_for_intermediate_example/genes/orphan1.gene
src/ruffus/test/data_for_intermediate_example/genes/orphan2.gwas
src/ruffus/test/data_for_intermediate_example/genes/orphan3.gwas
src/ruffus/test/data_for_intermediate_example/simulation/001.simulation
src/ruffus/test/data_for_intermediate_example/simulation/002.simulation
src/ruffus/test/data_for_intermediate_example/simulation/003.simulation
src/ruffus/test/data_for_intermediate_example/simulation/004.simulation
src/ruffus/test/data_for_intermediate_example/simulation/005.simulation
src/ruffus/test/data_for_intermediate_example/simulation/006.simulation
src/ruffus/test/data_for_intermediate_example/simulation/007.simulation
src/ruffus/test/data_for_intermediate_example/simulation/008.simulation
src/ruffus/test/data_for_intermediate_example/simulation/009.simulation
src/ruffus/test/data_for_intermediate_example/simulation/010.simulation
src/ruffus/test/data_for_intermediate_example/simulation/011.simulation
src/ruffus/test/data_for_intermediate_example/simulation/012.simulation
src/ruffus/test/data_for_intermediate_example/simulation/013.simulation
src/ruffus/test/data_for_intermediate_example/simulation/014.simulation
src/ruffus/test/data_for_intermediate_example/simulation/015.simulation
src/ruffus/test/data_for_intermediate_example/simulation/016.simulation
src/ruffus/test/data_for_intermediate_example/simulation/017.simulation
src/ruffus/test/data_for_intermediate_example/simulation/018.simulation
src/ruffus/test/data_for_intermediate_example/simulation/019.simulation
src/ruffus/test/data_for_intermediate_example/simulation/020.simulation
src/ruffus/test/data_for_intermediate_example/simulation/021.simulation
src/ruffus/test/data_for_intermediate_example/simulation/022.simulation
src/ruffus/test/data_for_intermediate_example/simulation/023.simulation
src/ruffus/test/data_for_intermediate_example/simulation/024.simulation
src/ruffus/test/data_for_intermediate_example/simulation/025.simulation
src/ruffus/test/data_for_intermediate_example/simulation/026.simulation
src/ruffus/test/data_for_intermediate_example/simulation/027.simulation
src/ruffus/test/data_for_intermediate_example/simulation/028.simulation
src/ruffus/test/data_for_intermediate_example/simulation/029.simulation
src/ruffus/test/data_for_intermediate_example/simulation/030.simulation
src/ruffus/test/data_for_intermediate_example/simulation/031.simulation
src/ruffus/test/data_for_intermediate_example/simulation/032.simulation
src/ruffus/test/data_for_intermediate_example/simulation/033.simulation
src/ruffus/test/data_for_intermediate_example/simulation/034.simulation
src/ruffus/test/data_for_intermediate_example/simulation/035.simulation
src/ruffus/test/data_for_intermediate_example/simulation/036.simulation
src/ruffus/test/data_for_intermediate_example/simulation/037.simulation
src/ruffus/test/data_for_intermediate_example/simulation/038.simulation
src/ruffus/test/data_for_intermediate_example/simulation/039.simulation
src/ruffus/test/data_for_intermediate_example/simulation/040.simulation
src/ruffus/test/data_for_intermediate_example/simulation/041.simulation
src/ruffus/test/data_for_intermediate_example/simulation/042.simulation
src/ruffus/test/data_for_intermediate_example/simulation/043.simulation
src/ruffus/test/data_for_intermediate_example/simulation/044.simulation
src/ruffus/test/data_for_intermediate_example/simulation/045.simulation
src/ruffus/test/data_for_intermediate_example/simulation/046.simulation
src/ruffus/test/data_for_intermediate_example/simulation/047.simulation
src/ruffus/test/data_for_intermediate_example/simulation/048.simulation
src/ruffus/test/data_for_intermediate_example/simulation/049.simulation
src/ruffus/test/data_for_intermediate_example/simulation/050.simulation
src/ruffus/test/data_for_intermediate_example/simulation/051.simulation
src/ruffus/test/data_for_intermediate_example/simulation/052.simulation
src/ruffus/test/data_for_intermediate_example/simulation/053.simulation
src/ruffus/test/data_for_intermediate_example/simulation/054.simulation
src/ruffus/test/data_for_intermediate_example/simulation/055.simulation
src/ruffus/test/data_for_intermediate_example/simulation/056.simulation
src/ruffus/test/data_for_intermediate_example/simulation/057.simulation
src/ruffus/test/data_for_intermediate_example/simulation/058.simulation
src/ruffus/test/data_for_intermediate_example/simulation/059.simulation
src/ruffus/test/data_for_intermediate_example/simulation/060.simulation
src/ruffus/test/data_for_intermediate_example/simulation/061.simulation
src/ruffus/test/data_for_intermediate_example/simulation/062.simulation
src/ruffus/test/data_for_intermediate_example/simulation/063.simulation
src/ruffus/test/data_for_intermediate_example/simulation/064.simulation
src/ruffus/test/data_for_intermediate_example/simulation/065.simulation
src/ruffus/test/data_for_intermediate_example/simulation/066.simulation
src/ruffus/test/data_for_intermediate_example/simulation/067.simulation
src/ruffus/test/data_for_intermediate_example/simulation/068.simulation
src/ruffus/test/data_for_intermediate_example/simulation/069.simulation
src/ruffus/test/data_for_intermediate_example/simulation/070.simulation
src/ruffus/test/data_for_intermediate_example/simulation/071.simulation
src/ruffus/test/data_for_intermediate_example/simulation/072.simulation
src/ruffus/test/data_for_intermediate_example/simulation/073.simulation
src/ruffus/test/data_for_intermediate_example/simulation/074.simulation
src/ruffus/test/data_for_intermediate_example/simulation/075.simulation
src/ruffus/test/data_for_intermediate_example/simulation/076.simulation
src/ruffus/test/data_for_intermediate_example/simulation/077.simulation
src/ruffus/test/data_for_intermediate_example/simulation/078.simulation
src/ruffus/test/data_for_intermediate_example/simulation/079.simulation
src/ruffus/test/data_for_intermediate_example/simulation/080.simulation
src/ruffus/test/data_for_intermediate_example/simulation/081.simulation
src/ruffus/test/data_for_intermediate_example/simulation/082.simulation
src/ruffus/test/data_for_intermediate_example/simulation/083.simulation
src/ruffus/test/data_for_intermediate_example/simulation/084.simulation
src/ruffus/test/data_for_intermediate_example/simulation/085.simulation
src/ruffus/test/data_for_intermediate_example/simulation/086.simulation
src/ruffus/test/data_for_intermediate_example/simulation/087.simulation
src/ruffus/test/data_for_intermediate_example/simulation/088.simulation
src/ruffus/test/data_for_intermediate_example/simulation/089.simulation
src/ruffus/test/data_for_intermediate_example/simulation/090.simulation
src/ruffus/test/data_for_intermediate_example/simulation/091.simulation
src/ruffus/test/data_for_intermediate_example/simulation/092.simulation
src/ruffus/test/data_for_intermediate_example/simulation/093.simulation
src/ruffus/test/data_for_intermediate_example/simulation/094.simulation
src/ruffus/test/data_for_intermediate_example/simulation/095.simulation
src/ruffus/test/data_for_intermediate_example/simulation/096.simulation
src/ruffus/test/data_for_intermediate_example/simulation/097.simulation
src/ruffus/test/data_for_intermediate_example/simulation/098.simulation
src/ruffus/test/data_for_intermediate_example/simulation/099.simulation
src/ruffus/test/data_for_intermediate_example/simulation/100.simulation
src/ruffus/test/data_for_intermediate_example/simulation/101.simulation
src/ruffus/test/data_for_intermediate_example/simulation/102.simulation
src/ruffus/test/data_for_intermediate_example/simulation/103.simulation
src/ruffus/test/data_for_intermediate_example/simulation/104.simulation
src/ruffus/test/dependency_data/dag.dependency
src/ruffus/test/dependency_data/non_dag.dependency
src/ruffus/test/dependency_data/simple.dag
src/ruffus/test/dependency_data/simpler.dag
src/ruffus/test/qrsh_workaround/output.1
src/ruffus/test/qrsh_workaround/output.10
src/ruffus/test/qrsh_workaround/output.2
src/ruffus/test/qrsh_workaround/output.3
src/ruffus/test/qrsh_workaround/output.4
src/ruffus/test/qrsh_workaround/output.5
src/ruffus/test/qrsh_workaround/output.6
src/ruffus/test/qrsh_workaround/output.7
src/ruffus/test/qrsh_workaround/output.8
src/ruffus/test/qrsh_workaround/output.9